[ALS-12763] Fix V3 Query Authorization - #753
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Replace the legacy resource-UUID + /proxy URL scheme with the new
gateway's clean per-service path prefixes (spec sections 3.3/3.4/3.7).
- /proxy/{container} relay -> clean prefixes: /dictionary, /uploader,
/visualization; the server-side log proxy now posts to /logging/audit.
- HPDS backend selection moves from resourceUUID in the query body to
the URL path: /hpds/auth (direct) vs /hpds/open (aggregate/obfuscated).
QueryOpenSync now targets /hpds/open/query/sync (open backend is built).
- Remove the non-federated single-resource UUID fork from Resources.ts
(hpdsAuth/hpdsOpen/hpdsOpenV3/search/visualization/aggregate and their
VITE_RESOURCE_* reads); the path selects the backend. The federated
site registry (queryable/getResources) is retained untouched.
- Search keeps its ignored {resourceId} segment via a nil placeholder.
- Update unit fixtures: Resources.test.ts (new getQueryResources
contract) and the log server proxy test (current /logging behavior).
Flagged for follow-up (see PR): the deployed gateway has no /visualization
route yet; federated discovery still uses the registry; the Playwright
e2e route mocks still assert the old URL scheme.
…alues path
The query-service dropped the registry-era {resourceId} placeholder
segment, so the nil-UUID constant and the trailing-slash values path go
away: Picsure.SearchValues = picsure/hpds/auth/search/values. Requires
the matching query-service change (monorepo 218d14c7).
The gateway /visualization route is live and the viz service accepts UUID-less requests, so both GATEWAY GAP notes are obsolete. .env.example: remove the dead resource-UUID entries (HPDS, OPEN_HPDS, OPEN_V3_HPDS, BASE_QUERY, VIZ — nothing reads them; Playwright tests use .env.test); document the two still-live ones where they belong: VITE_RESOURCE_APP (PSAMA query template) and VITE_RESOURCE_QUERY_ID_GEN (federated GIC queries).
Drop pointers to private design-spec section numbers from paths.ts and Resources.ts comments; the technical explanation is unchanged.
The field is gone from the visualization service's request model; the HPDS backend is chosen by path and access type comes from the gateway.
Open-access (Discover) stats are built as V3 requests via getQueryRequestV3 (phenotypicClause/genomicFilters/authorizationFilters) but were POSTed to the V1 open path /hpds/open/query/sync. The V1 aggregate controller forwards that V3 body to HPDS's V1 /PIC-SURE/query/sync, which cannot parse it, so the query-service returns 502 upstream_unavailable and Discover queries fail. Rename QueryOpenSync -> QueryOpenV3Sync and point it at /hpds/open/v3/query/sync so the body shape matches the endpoint, mirroring the auth side's QueryV3Sync.
## Summary - remove `resourceUUID` from V2 and V3 query request interfaces and serialized envelopes - remove the UUID parameter from query builders and count-provider request construction - migrate statistics, SNP, variant, visualization/export state, and cross-count callers to the path-routed request contract - remove resource UUIDs from statistics logging and its now-unused request plumbing - retain provider-level coverage proving provider-built requests omit `resourceUUID` ## Why The gateway now selects the HPDS backend from the request path. Query bodies no longer need a resource UUID for routing, and retaining it in builder APIs or statistics logging makes the old routing contract appear active. ## Validation - `pnpm run test:unit` - 343 passed - `pnpm vitest run src/routes/api/v1/log/server.test.ts` - 8 passed - `pnpm run check` - 0 errors and 0 warnings - `pnpm run build` - passed - Prettier and ESLint on changed files, plus `git diff --check` - passed The complete `pnpm test` workflow reached Playwright after its Vitest phase passed, then encountered the existing advanced-filtering setup failure where explorer search options do not load. The representative `AF-CORE-001` failure reproduces on the unchanged `pic_sure_api_rewrite` base in Chromium and Firefox. The remaining Playwright cases were stopped after confirming the baseline failure. Full-repository `pnpm run lint` currently stops on existing Prettier formatting in unchanged `tests/unit/Resources.test.ts`; the same file fails the formatter when read directly from `pic_sure_api_rewrite`. Supersedes #728, which GitHub automatically closed when its cross-fork head branch was renamed.
Co-authored-by: James <Jamestp19@gmail.com>
main's only unmerged commit, 92487e5 ([ALS-10701][ALS-10697] Use PSAMA consents endpoint), is already present here in adapted form, so this merge carries no content: the resulting tree is identical to 97a2bf0. All nine conflicts were this branch's own later work, and were resolved by keeping it: paths.ts HPDS_AUTH/HPDS_OPEN split and the open-access V3 sync path (02502f7) SNPFilter, VariantExplorer, Visualizations, ExportStepper, QueryBuilder, StatBuilder resource UUID removed from query requests (f4528dd, 0561f1d) stores/User.ts, tests/unit/Consents.test.ts stale-consents guard and its tests (97a2bf0) Recorded so the merge-base advances past 92487e5 and future merges from main do not re-present these settled conflicts.
The pnpm@11.5.3 packageManager field added in c25f0e7 conflicts with the version: 10 input that .github/workflows/tests.yml passes to pnpm/action-setup in all 7 jobs. The action throws when the two disagree, so setup and audit failed before running anything and every downstream job was skipped. main carries no packageManager field, which is why no other PR hits this. Dropping it restores parity with main and leaves the shared workflow untouched.
The path migration in src/lib/paths.ts moved the client's API routes but
left the Playwright mocks intercepting the old ones, so page.route() never
matched, requests escaped the mock layer, and the app rendered its error
state instead of data. Every affected spec failed on a missing <tbody>.
picsure/v3/query/sync -> picsure/hpds/auth/v3/query/sync
picsure/v3/query -> picsure/hpds/auth/v3/query
picsure/query/sync -> picsure/hpds/open/v3/query/sync
picsure/proxy/dictionary-api -> picsure/dictionary
picsure/proxy/visualization -> picsure/visualization
picsure/search/{HPDS}/values/ -> picsure/hpds/auth/search/values
The search mocks are not a prefix swap: path-based routing removed the
resource UUID (getCountResource now returns uuid: ''), and the request
drops the trailing slash before the query string. That left HPDS unused
in 5 specs; mock-data.ts keeps it for response payloads.
The open-access count endpoint also moved from V2 to V3, not just to a
new path. Response shapes are plain counts, matching what the auth V3
mocks already return.
1469 passed, 1 flaky (webkit drag-and-drop, green on retry), 0 failed.
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This repository does not receive automatic reviews because it has fewer than 10 stars. ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Pro Plus Run ID: 📝 WalkthroughWalkthroughThe PR adds consent-denied error detection, preserves sessions for those responses, routes visualization requests by access mode, and displays a shared consent message in dataset and export flows. ChangesConsent handling and visualization routing
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: 🔵 Low · up to Consent-denied responses with non-default messages may be presented as generic errors in dataset, download, and PFB export flows. The change is otherwise mergeable with explicit owner awareness and follow-up to preserve consistent consent-error handling. Suggested reviewers: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 14.29% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 7 functions across 6 files. (4 skipped: 4 unsupported.) ✨ Finishing Touches 💡 2📝 Generate docstrings 💡
🛠️ Fix failing CI checks 💡
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…thorization # Conflicts: # src/lib/components/explorer/Visualizations.svelte # tests/end-to-end/discover/distributions/test.ts # tests/end-to-end/explorer/export/test.ts # tests/end-to-end/explorer/visualizations/test.ts # tests/end-to-end/mock-data.ts
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In `@src/lib/api.ts`:
- Around line 17-19: Update consentDeniedMessage and isConsentDeniedError so
consent-denied errors remain identifiable when body.message is a non-default
string, using a stable marker or typed consent error while preserving the server
message. Add coverage for an errorType of consent_denied with a custom message
and verify the dataset, download, and PFB export flows take their consent-denied
branches.
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src/lib/api.tssrc/lib/components/explorer/Visualizations.sveltesrc/lib/components/explorer/export/DownloadButton.sveltesrc/lib/components/explorer/export/PfbExport.sveltesrc/lib/paths.tssrc/routes/(picsure)/(authorized)/dataset/[uuid]/+page.sveltetests/end-to-end/discover/distributions/test.tstests/end-to-end/explorer/visualizations/test.tstests/unit/api.test.tstests/unit/paths.test.ts
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JamesPeck
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Aug 27, 2026
isConsentDeniedError read `.message`, but SvelteKit's `error()` throws an HttpError that keeps its text at `body.message` and has no `message` of its own. It therefore returned false for every denial, not just the ones with a custom message, so the dataset page, download button, and PFB export all took their generic-error branches. The unit mock threw a plain Error, which is why this passed CI. Throw a typed body carrying `errorType: 'consent_denied'` and match on that marker, so wording the server chooses no longer decides whether a denial is recognized. Consumers now show the server's message and fall back to CONSENT_DENIED_MESSAGE. Also keep the 401/403 else-if chain intact, per review. A Response body can be read once, so the 403 branch reads it and ends itself through the extracted fail(), and the tail reads it only for the statuses that reach there. consentError.test.ts leaves @sveltejs/kit unmocked so error() throws a real HttpError. Four of its cases fail against the old predicate.
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Summary by CodeRabbit
New Features
Bug Fixes
Tests